EP4289996A3 - Techniques d'indexation d'acide nucléique - Google Patents

Techniques d'indexation d'acide nucléique Download PDF

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Publication number
EP4289996A3
EP4289996A3 EP23205539.2A EP23205539A EP4289996A3 EP 4289996 A3 EP4289996 A3 EP 4289996A3 EP 23205539 A EP23205539 A EP 23205539A EP 4289996 A3 EP4289996 A3 EP 4289996A3
Authority
EP
European Patent Office
Prior art keywords
nucleic acid
index
indexed
acid fragments
techniques
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP23205539.2A
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German (de)
English (en)
Other versions
EP4289996A2 (fr
Inventor
designation of the inventor has not yet been filed The
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Illumina Inc
Original Assignee
Illumina Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of EP4289996A2 publication Critical patent/EP4289996A2/fr
Publication of EP4289996A3 publication Critical patent/EP4289996A3/fr
Pending legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1072—Differential gene expression library synthesis, e.g. subtracted libraries, differential screening
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G16B35/10—Design of libraries
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Microbiology (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Library & Information Science (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Saccharide Compounds (AREA)
  • Mechanical Treatment Of Semiconductor (AREA)
EP23205539.2A 2017-11-06 2018-11-05 Techniques d'indexation d'acide nucléique Pending EP4289996A3 (fr)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762582175P 2017-11-06 2017-11-06
EP18804892.0A EP3707723B1 (fr) 2017-11-06 2018-11-05 Techniques d'indexation d'acide nucléique
PCT/US2018/059255 WO2019090251A2 (fr) 2017-11-06 2018-11-05 Techniques d'indexation d'acide nucléique

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
EP18804892.0A Division EP3707723B1 (fr) 2017-11-06 2018-11-05 Techniques d'indexation d'acide nucléique

Publications (2)

Publication Number Publication Date
EP4289996A2 EP4289996A2 (fr) 2023-12-13
EP4289996A3 true EP4289996A3 (fr) 2024-01-17

Family

ID=64362766

Family Applications (2)

Application Number Title Priority Date Filing Date
EP18804892.0A Active EP3707723B1 (fr) 2017-11-06 2018-11-05 Techniques d'indexation d'acide nucléique
EP23205539.2A Pending EP4289996A3 (fr) 2017-11-06 2018-11-05 Techniques d'indexation d'acide nucléique

Family Applications Before (1)

Application Number Title Priority Date Filing Date
EP18804892.0A Active EP3707723B1 (fr) 2017-11-06 2018-11-05 Techniques d'indexation d'acide nucléique

Country Status (12)

Country Link
US (2) US11891600B2 (fr)
EP (2) EP3707723B1 (fr)
JP (2) JP7091372B2 (fr)
KR (2) KR20230028569A (fr)
CN (1) CN110800064B (fr)
AU (2) AU2018359670B2 (fr)
CA (2) CA3067421C (fr)
DK (1) DK3707723T3 (fr)
ES (1) ES2966831T3 (fr)
FI (1) FI3707723T3 (fr)
IL (1) IL271239A (fr)
WO (1) WO2019090251A2 (fr)

Families Citing this family (12)

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US11783917B2 (en) 2019-03-21 2023-10-10 Illumina, Inc. Artificial intelligence-based base calling
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
US20210265009A1 (en) 2020-02-20 2021-08-26 Illumina, Inc. Artificial Intelligence-Based Base Calling of Index Sequences
WO2021168353A2 (fr) 2020-02-20 2021-08-26 Illumina, Inc. Appel de base de plusieurs à plusieurs basé sur l'intelligence artificielle
KR102482668B1 (ko) * 2020-03-10 2022-12-29 사회복지법인 삼성생명공익재단 고유 분자 식별자의 표지 정확도를 증진하는 방법
US11248265B1 (en) 2020-11-19 2022-02-15 Clear Labs, Inc Systems and processes for distinguishing pathogenic and non-pathogenic sequences from specimens
US20220336054A1 (en) 2021-04-15 2022-10-20 Illumina, Inc. Deep Convolutional Neural Networks to Predict Variant Pathogenicity using Three-Dimensional (3D) Protein Structures
US20230005253A1 (en) 2021-07-01 2023-01-05 Illumina, Inc. Efficient artificial intelligence-based base calling of index sequences
US20230183799A1 (en) * 2021-12-10 2023-06-15 Illumina, Inc. Parallel sample and index sequencing
WO2023175018A1 (fr) * 2022-03-15 2023-09-21 Illumina, Inc. Séquençage simultané des brins sens et antisens du complément sur des polynucléotides séparés
WO2024081805A1 (fr) * 2022-10-13 2024-04-18 Element Biosciences, Inc. Séparation de données de séquençage en parallèle avec un cycle de séquençage dans une analyse de données de séquençage nouvelle génération

Citations (8)

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Publication number Priority date Publication date Assignee Title
WO2011100617A2 (fr) * 2010-02-12 2011-08-18 Life Technologies Corporation Codes d'identification d'acides nucléiques, de biomolécules et de polymères
US20130231253A1 (en) * 2012-01-26 2013-09-05 Doug Amorese Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library regeneration
WO2014062717A1 (fr) * 2012-10-15 2014-04-24 Life Technologies Corporation Compositions, procédés, systèmes et kits pour l'enrichissement d'acides nucléiques cibles
US20160017320A1 (en) * 2014-07-15 2016-01-21 Qiagen Sciences, Llc Semi-random barcodes for nucleic acid analysis
WO2016022833A1 (fr) * 2014-08-06 2016-02-11 Nugen Technologies, Inc. Mesures numériques à partir de séquençage ciblé
US20160122753A1 (en) * 2013-06-12 2016-05-05 Tarjei Mikkelsen High-throughput rna-seq
US20160314242A1 (en) * 2015-04-23 2016-10-27 10X Genomics, Inc. Sample indexing methods and compositions for sequencing applications
US20160319345A1 (en) * 2015-04-28 2016-11-03 Illumina, Inc. Error suppression in sequenced dna fragments using redundant reads with unique molecular indices (umis)

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US5750341A (en) 1995-04-17 1998-05-12 Lynx Therapeutics, Inc. DNA sequencing by parallel oligonucleotide extensions
ATE545710T1 (de) 1997-04-01 2012-03-15 Illumina Cambridge Ltd Verfahren zur vervielfältigung von nukleinsäuren
US6969488B2 (en) 1998-05-22 2005-11-29 Solexa, Inc. System and apparatus for sequential processing of analytes
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
EP3002289B1 (fr) 2002-08-23 2018-02-28 Illumina Cambridge Limited Nucleotides modifies pour le sequençage de polynucleotide
GB0321306D0 (en) 2003-09-11 2003-10-15 Solexa Ltd Modified polymerases for improved incorporation of nucleotide analogues
ES2949821T3 (es) 2004-01-07 2023-10-03 Illumina Cambridge Ltd Matrices moleculares
EP1828412B2 (fr) 2004-12-13 2019-01-09 Illumina Cambridge Limited Procede ameliore de detection de nucleotides
WO2006120433A1 (fr) 2005-05-10 2006-11-16 Solexa Limited Polymerases ameliorees
GB0514936D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Preparation of templates for nucleic acid sequencing
US7329860B2 (en) 2005-11-23 2008-02-12 Illumina, Inc. Confocal imaging methods and apparatus
US7754429B2 (en) * 2006-10-06 2010-07-13 Illumina Cambridge Limited Method for pair-wise sequencing a plurity of target polynucleotides
EP2092322B1 (fr) 2006-12-14 2016-02-17 Life Technologies Corporation Procédés et appareil permettant de mesurer des analytes en utilisant des matrices de tec à grande échelle
US8349167B2 (en) 2006-12-14 2013-01-08 Life Technologies Corporation Methods and apparatus for detecting molecular interactions using FET arrays
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JP4337919B2 (ja) 2007-07-06 2009-09-30 トヨタ自動車株式会社 設計支援装置、方法及びプログラム
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EP4234713A3 (fr) 2012-03-20 2024-02-14 University Of Washington Through Its Center For Commercialization Méthodes permettant de faire baisser le taux d'erreurs observées lors d'un séquençage massif d'adn eu parallèle en faisant appel à un séquençage par consensus duplex
EP4001427A1 (fr) 2012-04-24 2022-05-25 Gen9, Inc. Procédés de tri d'acides nucléiques et de clonage in vitro multiplex préparatoire
WO2013181170A1 (fr) 2012-05-31 2013-12-05 Board Of Regents, The University Of Texas System Procédé de séquençage précis d'adn
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WO2011100617A2 (fr) * 2010-02-12 2011-08-18 Life Technologies Corporation Codes d'identification d'acides nucléiques, de biomolécules et de polymères
US20130231253A1 (en) * 2012-01-26 2013-09-05 Doug Amorese Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library regeneration
WO2014062717A1 (fr) * 2012-10-15 2014-04-24 Life Technologies Corporation Compositions, procédés, systèmes et kits pour l'enrichissement d'acides nucléiques cibles
US20160122753A1 (en) * 2013-06-12 2016-05-05 Tarjei Mikkelsen High-throughput rna-seq
US20160017320A1 (en) * 2014-07-15 2016-01-21 Qiagen Sciences, Llc Semi-random barcodes for nucleic acid analysis
WO2016022833A1 (fr) * 2014-08-06 2016-02-11 Nugen Technologies, Inc. Mesures numériques à partir de séquençage ciblé
US20160314242A1 (en) * 2015-04-23 2016-10-27 10X Genomics, Inc. Sample indexing methods and compositions for sequencing applications
US20160319345A1 (en) * 2015-04-28 2016-11-03 Illumina, Inc. Error suppression in sequenced dna fragments using redundant reads with unique molecular indices (umis)

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Also Published As

Publication number Publication date
AU2021266189A1 (en) 2021-12-02
JP2022126742A (ja) 2022-08-30
IL271239A (en) 2020-01-30
CN110800064B (zh) 2024-03-29
US20240117341A1 (en) 2024-04-11
US11891600B2 (en) 2024-02-06
KR20230028569A (ko) 2023-02-28
JP7091372B2 (ja) 2022-06-27
EP3707723A2 (fr) 2020-09-16
KR20200005607A (ko) 2020-01-15
AU2018359670A1 (en) 2019-11-21
KR102500210B1 (ko) 2023-02-15
AU2018359670B2 (en) 2021-08-26
DK3707723T3 (da) 2023-12-18
CA3067421A1 (fr) 2019-05-09
WO2019090251A3 (fr) 2020-01-16
CA3067421C (fr) 2023-08-15
US20190218545A1 (en) 2019-07-18
CN110800064A (zh) 2020-02-14
FI3707723T3 (fi) 2023-12-13
WO2019090251A2 (fr) 2019-05-09
CA3202587A1 (fr) 2019-05-09
ES2966831T3 (es) 2024-04-24
JP2020528741A (ja) 2020-10-01
EP4289996A2 (fr) 2023-12-13
EP3707723B1 (fr) 2023-10-25

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